[sbml-discuss] SpeciesConcentrationRule and Modifiers

rmachne rmachne at meta.lo-res.org
Thu Feb 3 15:37:08 PST 2005


> Many models use dummy molecular species whose concentration is the sum 
> of concentrations of other molecules, e.g.,  A = B + C + D.
...
> As an aside, the odeSolver by Rainer Machne quite happily solves such
> models correctly even if the dummy molecules are not treated as 
> modifiers. 
>

The odeSolver just replaces A by (B+C+D) in all other formulas, and has no 
calculation for A itself (except for print out of A's concentration), 
which I hope is a correct interpretation of SBML's intention.

If A is e.g. substrate of a reaction, this has no effect on A, B, C and 
D's concentrations.

If I am correct, this construct can not be used in your models, for e.g. 
comprehending all the active states of PKC into one dummy species, because 
active PKC build a complex with their substrates and this would consume 
PKC, which cannot be used for the backward reactions (to the inactive PKC 
states).
I had some ideas, but I couldn't come up with an SBML construct yet, that 
would express this correctly, except for treating each active PKC 
species separately.

I hope that helps,
Rainer







On Wed, 2 Feb 2005, Upinder S. Bhalla wrote:

> Hi,
>  We are tidying up some loose ends with the kinetikit (.g) to SBML
> converter.
> We would like to know how to handle the following situation:
>
> Many models use dummy molecular species whose concentration is the sum of
> concentrations of other molecules, e.g.,  A = B + C + D.
> This is easy to express as a SpeciesConcentrationRule. One of the
> conditions of the rule in SBML level 2 is that the species to which it
> applies should not be consumed or produced by a reaction. So, am I correct
> in assuming then that the dummy species (A in the example) should be used
> as a modifier in reactions in which it participates?
>
> As an aside, the odeSolver by Rainer Machne quite happily solves such
> models correctly even if the dummy molecules are not treated as modifiers.
>
> Thanks,
>  Upi Bhalla
> --
> Upinder S. Bhalla        National Centre for
> bhalla at ncbs.res.in       Biological Sciences, TIFR
> +91-80-2363-6420X3230    UAS-GKVK Campus
> Fax: +91-80-23636662     Bangalore 560065, INDIA
> Web: http://www.ncbs.res.in/~faculty/upi.html
>
>
>
>



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